Alignments for a candidate for metC in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for metC in Sinorhizobium medicae WSM419

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate YP_001325828.1 Smed_0133 O-succinylhomoserine sulfhydrylase

Query= BRENDA::Q5H4T8
         (397 letters)



>NCBI__GCF_000017145.1:YP_001325828.1
          Length = 394

 Score =  241 bits (615), Expect = 3e-68
 Identities = 146/384 (38%), Positives = 223/384 (58%), Gaps = 10/384 (2%)

Query: 18  ATLAIHGG----QSPDPSTGAVMPP--IYATSTYAQSS-PGEHQGFEYSRTHNPTRFAYE 70
           AT  +HGG    Q  + S    +    +Y TS  A++   GE  G+ Y+R  +PT   +E
Sbjct: 8   ATQLVHGGTLRSQYGETSEAIFLTQGFVYDTSEAAEARFKGETDGYIYARYGSPTNDMFE 67

Query: 71  RCVAALEGGTRAFAFASGMAATST-VMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129
           + +  LEG   A A ASGMAA S  ++  + AG H+VA   L+G    + E +  +  G+
Sbjct: 68  KRMCMLEGAEDARATASGMAAVSAAILCQVKAGDHIVAARALFGSCRWVVETLAPKY-GV 126

Query: 130 DFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFA 189
           + + VD  D   ++ A+R +TK+ ++E+PTNP L+++DIA +A +A + G   VVDN FA
Sbjct: 127 ECTLVDGRDLKNWEDAVRPNTKVFFLESPTNPTLEVIDIAGVARLADQIGAKVVVDNVFA 186

Query: 190 SPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPF 249
           +P+ Q+PL LGA +VV+SATK+++G    +GG+ V+ D   + E +       G    PF
Sbjct: 187 TPLFQKPLELGAHIVVYSATKHIDGQGRCLGGV-VLSDKQWIDENLHDYFRHTGPAMSPF 245

Query: 250 DSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGF 309
           +++  L+G++TLPLR+R   E+A  +A +L   P + +VIYPG   HPQ  +  +QMSG 
Sbjct: 246 NAWTLLKGIETLPLRVRQQTESARRIADFLTEQPQVARVIYPGRKDHPQADIIAKQMSGG 305

Query: 310 GGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGIS 369
             +V+  LKGG +AA       E+  ++ +LG  +SL+ HPA  TH ++    R +LGIS
Sbjct: 306 STLVAFELKGGKEAAFALQNALEIVRISNNLGDSKSLITHPATTTHKNLTDEARAELGIS 365

Query: 370 DALVRLSVGIEDLGDLRGDLERAL 393
              VR S GIED  DL  D  +AL
Sbjct: 366 AGTVRFSAGIEDSEDLVEDFAKAL 389


Lambda     K      H
   0.320    0.134    0.391 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 387
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 397
Length of database: 394
Length adjustment: 31
Effective length of query: 366
Effective length of database: 363
Effective search space:   132858
Effective search space used:   132858
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis